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Póvoa P, Coelho L, Cidade JP, Ceccato A, Morris AC, Salluh J, Nobre V, Nseir S, Martin-Loeches I, Lisboa T, Ramirez P, Rouzé A, Sweeney DA, Kalil AC. Biomarkers in pulmonary infections: a clinical approach. Ann Intensive Care 2024; 14:113. [PMID: 39020244 PMCID: PMC11254884 DOI: 10.1186/s13613-024-01323-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/27/2024] [Indexed: 07/19/2024] Open
Abstract
Severe acute respiratory infections, such as community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia, constitute frequent and lethal pulmonary infections in the intensive care unit (ICU). Despite optimal management with early appropriate empiric antimicrobial therapy and adequate supportive care, mortality remains high, in part attributable to the aging, growing number of comorbidities, and rising rates of multidrug resistance pathogens. Biomarkers have the potential to offer additional information that may further improve the management and outcome of pulmonary infections. Available pathogen-specific biomarkers, for example, Streptococcus pneumoniae urinary antigen test and galactomannan, can be helpful in the microbiologic diagnosis of pulmonary infection in ICU patients, improving the timing and appropriateness of empiric antimicrobial therapy since these tests have a short turnaround time in comparison to classic microbiology. On the other hand, host-response biomarkers, for example, C-reactive protein and procalcitonin, used in conjunction with the clinical data, may be useful in the diagnosis and prediction of pulmonary infections, monitoring the response to treatment, and guiding duration of antimicrobial therapy. The assessment of serial measurements overtime, kinetics of biomarkers, is more informative than a single value. The appropriate utilization of accurate pathogen-specific and host-response biomarkers may benefit clinical decision-making at the bedside and optimize antimicrobial stewardship.
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Affiliation(s)
- Pedro Póvoa
- Department of Intensive Care, Hospital de São Francisco Xavier, ULSLO, Lisbon, Portugal.
- NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Campo dos Mártires da Pátria 130, 1169-056, Lisbon, Portugal.
- Center for Clinical Epidemiology and Research Unit of Clinical Epidemiology, OUH Odense University Hospital, Odense, Denmark.
| | - Luís Coelho
- Department of Intensive Care, Hospital de São Francisco Xavier, ULSLO, Lisbon, Portugal
- Pulmonary Department, CDP Dr. Ribeiro Sanches, ULS Santa Maria, Lisbon, Portugal
| | - José Pedro Cidade
- Department of Intensive Care, Hospital de São Francisco Xavier, ULSLO, Lisbon, Portugal
- Center for Clinical Epidemiology and Research Unit of Clinical Epidemiology, OUH Odense University Hospital, Odense, Denmark
| | - Adrian Ceccato
- Critical Care Center, Institut d'Investigació i Innovació Parc Taulí I3PT-CERCA, Hospital Universitari Parc Taulí, Univeristat Autonoma de Barcelona, Sabadell, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Intensive Care Unit, Hospital Universitari Sagrat Cor, Grupo Quironsalud, Barcelona, Spain
| | - Andrew Conway Morris
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, UK
- JVF Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK
| | - Jorge Salluh
- Postgraduate Program, D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
- Postgraduate Program of Internal Medicine, Federal University of Rio de Janeiro, (UFRJ), Rio de Janeiro, Brazil
| | - Vandack Nobre
- School of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Saad Nseir
- 1Univ. Lille, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
- CNRS, UMR 8576, 59000, Lille, France
- INSERM, U1285, 59000, Lille, France
- CHU Lille, Service de Médecine Intensive Réanimation, 59000, Lille, France
| | - Ignacio Martin-Loeches
- Department of Intensive Care Medicine, Multidisciplinary Intensive Care Research Organization (MICRO), St. James Hospital, Dublin, Ireland
- Department of Pneumology, Hospital Clinic of Barcelona-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Thiago Lisboa
- Postgraduate Program Pulmonary Science, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Paula Ramirez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Department of Critical Care Medicine, Hospital Universitario Y Politécnico La Fe, Valencia, Spain
| | - Anahita Rouzé
- 1Univ. Lille, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
- CNRS, UMR 8576, 59000, Lille, France
- INSERM, U1285, 59000, Lille, France
- CHU Lille, Service de Médecine Intensive Réanimation, 59000, Lille, France
| | - Daniel A Sweeney
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, La Jolla, San Diego, CA, USA
| | - Andre C Kalil
- Department of Internal Medicine, Division of Infectious Diseases, University of Nebraska Medical Center, Omaha, NE, USA
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Das S, Kaminski TW, Schlegel BT, Bain W, Hu S, Patel A, Kale SL, Chen K, Lee JS, Mallampalli RK, Kagan VE, Rajasundaram D, McVerry BJ, Sundd P, Kitsios GD, Ray A, Ray P. Neutrophils and galectin-3 defend mice from lethal bacterial infection and humans from acute respiratory failure. Nat Commun 2024; 15:4724. [PMID: 38830855 PMCID: PMC11148175 DOI: 10.1038/s41467-024-48796-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
Respiratory infection by Pseudomonas aeruginosa, common in hospitalized immunocompromised and immunocompetent ventilated patients, can be life-threatening because of antibiotic resistance. This raises the question of whether the host's immune system can be educated to combat this bacterium. Here we show that prior exposure to a single low dose of lipopolysaccharide (LPS) protects mice from a lethal infection by P. aeruginosa. LPS exposure trained the innate immune system by promoting expansion of neutrophil and interstitial macrophage populations distinguishable from other immune cells with enrichment of gene sets for phagocytosis- and cell-killing-associated genes. The cell-killing gene set in the neutrophil population uniquely expressed Lgals3, which encodes the multifunctional antibacterial protein, galectin-3. Intravital imaging for bacterial phagocytosis, assessment of bacterial killing and neutrophil-associated galectin-3 protein levels together with use of galectin-3-deficient mice collectively highlight neutrophils and galectin-3 as central players in LPS-mediated protection. Patients with acute respiratory failure revealed significantly higher galectin-3 levels in endotracheal aspirates (ETAs) of survivors compared to non-survivors, galectin-3 levels strongly correlating with a neutrophil signature in the ETAs and a prognostically favorable hypoinflammatory plasma biomarker subphenotype. Taken together, our study provides impetus for harnessing the potential of galectin-3-expressing neutrophils to protect from lethal infections and respiratory failure.
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Affiliation(s)
- Sudipta Das
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine and Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Tomasz W Kaminski
- VERSITI Blood Research Institute and Medical College of Wisconsin, Milwaukee, WI, 53233, USA
| | - Brent T Schlegel
- Department of Pediatrics, Division of Health Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, USA
| | - William Bain
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine and Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Veteran's Affairs Pittsburgh Healthcare System, Pittsburgh, PA, 15240, USA
| | - Sanmei Hu
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine and Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Akruti Patel
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine and Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Sagar L Kale
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine and Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Kong Chen
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine and Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Janet S Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rama K Mallampalli
- Department of Medicine, The Ohio State University (OSU), Columbus, OH, 43210, USA
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, Division of Health Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine and Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Prithu Sundd
- VERSITI Blood Research Institute and Medical College of Wisconsin, Milwaukee, WI, 53233, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine and Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Anuradha Ray
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine and Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Prabir Ray
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine and Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
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Grudzinski KM, Fenske S, Wunderink RG, Gao CA. Neutrophil percentages in bronchoalveolar lavage fluid: Implications for diagnosing bacterial pneumonia in patients with immunocompromise and neutropenia. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.04.24306709. [PMID: 38766045 PMCID: PMC11100846 DOI: 10.1101/2024.05.04.24306709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Background Pneumonia is the leading cause of infectious deaths and the most common infection identified in ICU patients. Assessment of bronchoalveolar lavage fluid (BALF) cellularity can aid in pneumonia diagnosis. Low percentages (<50%) of BALF neutrophils have a high negative predictive value for bacterial pneumonia in a general medical ICU population, but unclear operating characteristics in patients with immunocompromise and neutropenia remain unknown. Methods We analyzed a large cohort of BALF specimens obtained for routine care for suspected pneumonia in mechanically ventilated patients and enrolled in the single-center Successful Clinical Response In Pneumonia Therapy (SCRIPT) study. BALF neutrophils were reported as a percentage of leukocytes by the clinical laboratory. The etiology of each episode of suspected pneumonia was adjudicated by a committee of critical care physicians using a predefined protocol. Immunocompromise was defined using predetermined criteria by the study research team. Neutropenia was defined here as a peripheral ANC <1500 cells/μl. Data are expressed as median [Quartile (Q) 1, Q3] and compared using the Mann-Whitney U test. Results 688 mechanically ventilated patients with suspected pneumonia were included. 409 (59.4%) were male; median age was 62 [51,71]. 461 patients (67.0%) were immunocompetent, 149 (21.7%) were immunocompromised without neutropenia and 78 (11.3%) were neutropenic at some point during their admission. A total of 1746 BALs were performed. Fifty-seven BALs were obtained on a day where the patient's ANC<1500. Amongst pneumonia episodes classified as bacterial, no difference was found amongst BALF percent neutrophils taken patients who were immunocompetent and those who were immunocompromised but not neutropenic on day of sampling: 84.0% [69.0, 93.0] vs 87.0% [68.3, 93.0], p = 0.878 (Figure 1B). However, BALF percent neutrophils were significantly lower in patients neutropenic on day of sampling, with median BALF percent neutrophils of only 65.0% [22.3, 70.5] (p=0.016 compared with immunocompromised group, p=0.0096 compared with immunocompetent group). Conclusion Among patients with bacterial pneumonia, BALF neutrophil percentage was not significantly decreased by a spectrum of immunocompromise. However, the subset of patients who were acutely neutropenic at the time of BAL sampling had significantly lower BALF % neutrophils. A traditional approach using BALF<50% to suggest against bacterial pneumonia may be inaccurate in this particular population.
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Affiliation(s)
- Kevin M. Grudzinski
- Department of Internal Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Samuel Fenske
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Richard G. Wunderink
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Catherine A. Gao
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, IL
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Gao CA, Markov NS, Pickens C, Pawlowski A, Kang M, Walter JM, Singer BD, Wunderink RG. An observational cohort study of bronchoalveolar lavage fluid galactomannan and Aspergillus culture positivity in patients requiring mechanical ventilation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.07.24302392. [PMID: 38370841 PMCID: PMC10871379 DOI: 10.1101/2024.02.07.24302392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Rationale Critically ill patients who develop invasive pulmonary aspergillosis (IPA) have high mortality rates despite antifungal therapy. Diagnosis is difficult in these patients. Bronchoalveolar lavage (BAL) fluid galactomannan (GM) is a helpful marker of infection, although the optimal cutoff for IPA is unclear. We aimed to evaluate the BAL fluid GM and fungal culture results, demographics, and outcomes among a large cohort of mechanically ventilated patients with suspected pneumonia. Methods A single-center cohort study of patients enrolled in the Successful Clinical Response in Pneumonia Therapy (SCRIPT) study from June 2018 to March 2023. Demographics, BAL results, and outcomes data were extracted from the electronic health record and compared between groups of patients who grew Aspergillus on a BAL fluid culture, those who had elevated BAL fluid GM levels (defined as >0.5 or >0.8) but did not grow Aspergillus on BAL fluid culture, and those with neither. Results Of over 1700 BAL samples from 688 patients, only 18 BAL samples grew Aspergillus. Patients who had a BAL sample grow Aspergillus (n=15) were older (median 71 vs 62 years, p=0.023), had more days intubated (29 vs 11, p=0.002), and more ICU days (34 vs 15, p=0.002) than patients whose BAL fluid culture was negative for Aspergillus (n=672). The BAL fluid galactomannan level was higher from samples that grew Aspergillus on culture than those that did not (median ODI 7.08 vs 0.11, p<0.001), though the elevation of BAL fluid GM varied across BAL samples for patients who had serial sampling. Patients who grew Aspergillus had a similar proportion of underlying immunocompromise compared with the patients who did not, and while no statistically significant difference in overall unfavorable outcome, had longer duration of ventilation and longer ICU stays. Conclusions In this large cohort of critically ill patients with a high number of BAL samples with GM levels, we found a relatively low rate of Aspergillus growth. Patients who eventually grew Aspergillus had inconsistently elevated BAL fluid GM, and many patients with elevated BAL fluid GM did not grow Aspergillus. These data suggest that the pre-test probability of invasive pulmonary aspergillosis should be considered low in a general ICU population undergoing BAL evaluation to define the etiology of pneumonia. Improved scoring systems are needed to enhance pre-test probability for diagnostic test stewardship purposes.
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Affiliation(s)
- Catherine A. Gao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nikolay S. Markov
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chiagozie Pickens
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Anna Pawlowski
- Northwestern Medicine Enterprise Data Warehouse, Chicago, IL, USA
| | - Mengjia Kang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - James M. Walter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Benjamin D. Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Richard G. Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Rabin EE, Walter JM, Wunderink RG, Qi C, Pickens CI. Clinical significance of culture-negative, PCR-positive bronchoalveolar lavage results in severe pneumonia. ERJ Open Res 2023; 9:00343-2023. [PMID: 37965226 PMCID: PMC10641578 DOI: 10.1183/23120541.00343-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/12/2023] [Indexed: 11/16/2023] Open
Abstract
Some culture-negative, PCR-positive BAL samples may represent true infection. A subset of patients with a culture-negative, PCR-positive BAL result will have a subsequent BAL culture positive for the organism initially identified by PCR alone. https://bit.ly/3DWoFPo.
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Affiliation(s)
- Erik E. Rabin
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - James M. Walter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Richard G. Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Chao Qi
- Department of Pathology, Northwestern Memorial Hospital, Chicago, IL, USA
| | - Chiagozie I. Pickens
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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Jovisic M, Mambetsariev N, Singer BD, Morales-Nebreda L. Differential roles of regulatory T cells in acute respiratory infections. J Clin Invest 2023; 133:e170505. [PMID: 37463441 PMCID: PMC10348770 DOI: 10.1172/jci170505] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Abstract
Acute respiratory infections trigger an inflammatory immune response with the goal of pathogen clearance; however, overexuberant inflammation causes tissue damage and impairs pulmonary function. CD4+FOXP3+ regulatory T cells (Tregs) interact with cells of both the innate and the adaptive immune system to limit acute pulmonary inflammation and promote its resolution. Tregs also provide tissue protection and coordinate lung tissue repair, facilitating a return to homeostatic pulmonary function. Here, we review Treg-mediated modulation of the host response to respiratory pathogens, focusing on mechanisms underlying how Tregs promote resolution of inflammation and repair of acute lung injury. We also discuss potential strategies to harness and optimize Tregs as a cellular therapy for patients with severe acute respiratory infection and discuss open questions in the field.
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Affiliation(s)
- Milica Jovisic
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
- Simpson Querrey Lung Institute for Translational Science
| | | | - Benjamin D. Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
- Simpson Querrey Lung Institute for Translational Science
- Department of Biochemistry and Molecular Genetics, and
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Luisa Morales-Nebreda
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
- Simpson Querrey Lung Institute for Translational Science
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Birkett R, Newar J, Sharma AM, Lin E, Blank L, Swaminathan S, Misharin A, Mestan KK. Development of a novel humanized mouse model to study bronchopulmonary dysplasia. Front Pediatr 2023; 11:1146014. [PMID: 37520051 PMCID: PMC10375491 DOI: 10.3389/fped.2023.1146014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Rationale The role of circulating fetal monocytes in bronchopulmonary dysplasia is not known. We utilized a humanized mouse model that supports human progenitor cell engraftment (MISTRG) to test the hypothesis that prenatal monocyte programming alters early lung development and response to hyperoxia. Methods Cord blood-derived monocytes from 10 human infants were adoptively transferred into newborn MISTRG mice at p0 (1 × 106 cells/mouse, intrahepatic injection) followed by normoxia versus hyperoxia (85% oxygen × 14 days). Lungs were harvested at p14 for alveolar histology (alveolar count, perimeter and area) and vascular parameters (vWF staining for microvessel density, Fulton's index). Human CD45 staining was conducted to compare presence of hematopoietic cells. Murine lung parameters were compared among placebo and monocyte-injected groups. The individual profiles of the 10 patients were further considered, including gestational age (GA; n = 2 term, n = 3 moderate/late preterm, and n = 5 very preterm infants) and preeclampsia (n = 4 patients). To explore the monocyte microenvironment of these patients, 30 cytokines/chemokines were measured in corresponding human plasma by multiplex immunoassay. Results Across the majority of patients and corresponding mice, MISTRG alveolarization was simplified and microvessel density was decreased following hyperoxia. Hyperoxia-induced changes were seen in both placebo (PBS) and monocyte-injected mice. Under normoxic conditions, alveolar development was altered modestly by monocytes as compared with placebo (P < 0.05). Monocyte injection was associated with increased microvessel density at P14 as compared with placebo (26.7 ± 0.73 vs. 18.8 ± 1.7 vessels per lung field; P < 0.001). Pooled analysis of patients revealed that injection of monocytes from births complicated by lower GA and preeclampsia was associated with changes in alveolarization and vascularization under normoxic conditions. These differences were modified by hyperoxia. CD45+ cell count was positively correlated with plasma monocyte chemoattractant protein-1 (P < 0.001) and macrophage inflammatory protein-1β (P < 0.01). Immunohistochemical staining for human CD206 and mouse F4/80 confirmed absence of macrophages in MISTRG lungs at P14. Conclusions Despite the inherent absence of macrophages in early stages of lung development, immunodeficient MISTRG mice revealed changes in alveolar and microvascular development induced by human monocytes. MISTRG mice exposed to neonatal hyperoxia may serve as a novel model to study isolated effects of human monocytes on alveolar and pulmonary vascular development.
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Affiliation(s)
- Rob Birkett
- Department of Pediatrics/Division of Neonatology, Ann & Robert H. Lurie Children’s Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Janu Newar
- Department of Pediatrics/Division of Neonatology, UC San Diego School of Medicine & Rady Children’s Hospital of San Diego, La Jolla, CA, United States
| | - Abhineet M. Sharma
- Department of Pediatrics/Division of Neonatology, Ann & Robert H. Lurie Children’s Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Erika Lin
- Department of Pediatrics/Division of Neonatology, UC San Diego School of Medicine & Rady Children’s Hospital of San Diego, La Jolla, CA, United States
| | - Lillian Blank
- Department of Pediatrics/Division of Neonatology, UC San Diego School of Medicine & Rady Children’s Hospital of San Diego, La Jolla, CA, United States
| | - Suchitra Swaminathan
- Department of Medicine/Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Alexander Misharin
- Department of Medicine/Division of Pulmonary & Critical Care, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Karen K. Mestan
- Department of Pediatrics/Division of Neonatology, Ann & Robert H. Lurie Children’s Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Pediatrics/Division of Neonatology, UC San Diego School of Medicine & Rady Children’s Hospital of San Diego, La Jolla, CA, United States
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Mikacenic C, Fussner LA, Bell J, Burnham EL, Chlan LL, Cook SK, Dickson RP, Almonor F, Luo F, Madan K, Morales-Nebreda L, Mould KJ, Simpson AJ, Singer BD, Stapleton RD, Wendt CH, Files DC. Research Bronchoscopies in Critically Ill Research Participants: An Official American Thoracic Society Workshop Report. Ann Am Thorac Soc 2023; 20:621-631. [PMID: 37125997 PMCID: PMC10174130 DOI: 10.1513/annalsats.202302-106st] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Bronchoscopy for research purposes is a valuable tool to understand lung-specific biology in human participants. Despite published reports and active research protocols using this procedure in critically ill patients, no recent document encapsulates the important safety considerations and downstream applications of this procedure in this setting. The objectives were to identify safe practices for patient selection and protection of hospital staff, provide recommendations for sample procurement to standardize studies, and give guidance on sample preparation for novel research technologies. Seventeen international experts in the management of critically ill patients, bronchoscopy in clinical and research settings, and experience in patient-oriented clinical or translational research convened for a workshop. Review of relevant literature, expert presentations, and discussion generated the findings presented herein. The committee concludes that research bronchoscopy with bronchoalveolar lavage in critically ill patients on mechanical ventilation is valuable and safe in appropriately selected patients. This report includes recommendations on standardization of this procedure and prioritizes the reporting of sample management to produce more reproducible results between laboratories. This document serves as a resource to the community of researchers who endeavor to include bronchoscopy as part of their research protocols and highlights key considerations for the inclusion and safety of research participants.
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A limited role for microbiological testing for childhood lower respiratory tract infections in primary care: managing diagnostic uncertainty by withholding antibiotics and watchful waiting. Clin Microbiol Infect 2022; 28:1189-1192. [PMID: 35738322 DOI: 10.1016/j.cmi.2022.06.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/20/2022]
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Cheng J, Ji D, Yin Y, Wang S, Song K, Pan Q, Zhang Q, Yang L. Proteomic profiling of serum small extracellular vesicles reveals immune signatures of children with pneumonia. Transl Pediatr 2022; 11:891-908. [PMID: 35800266 PMCID: PMC9253949 DOI: 10.21037/tp-22-134] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/01/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Pneumonia is the leading cause of death in young children globally. However, the underlying pathological mechanism of pediatric pneumonia remains unclear. In infection disease contexts, small extracellular vesicles (sEVs) have been shown to be a useful source of markers for pathogenesis and immune response. We hypothesized that functional molecules such as protein harbored by sEVs would provide mechanistic insights into the immune response in children with pneumonia. METHODS We isolated sEVs from serum collected from children with and without pneumonia, performed proteomic analysis of the sEVs with label-free mass spectrometry, and then conducted functional enrichment analysis of proteomic data. RESULTS We identified fifteen differentially expressed proteins and ten unique proteins in children with pneumonia as compared to healthy children. In the pneumonia group, immune-related processes and pathways were positively enriched as upregulated proteins were involved in neutrophil activation, complement regulation, defense against bacteria, humoral immune response and regulation of immune effector processes However, pathways associated with tissue development and extracellular matrix remodeling were negatively enriched, as downregulated proteins were linked to extracellular matrix structure and cell adhesions. CONCLUSIONS Our findings provided insights into host responses to pathogen infection, which has contributed to understanding the pathogenesis of children with pneumonia. Furthermore, our studies suggested that serum sEVs proteins could be considered a potential source of biomarkers for diagnosing pediatric pneumonia.
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Affiliation(s)
- Juan Cheng
- Department of Clinical Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongrui Ji
- Wayen Biotechnologies (Shanghai), Inc., Shanghai, China
| | - Yong Yin
- Department of Pulmonary Disease, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shidong Wang
- Wayen Biotechnologies (Shanghai), Inc., Shanghai, China
| | - Kai Song
- Wayen Biotechnologies (Shanghai), Inc., Shanghai, China
| | - Qiuhui Pan
- Department of Clinical Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qinghua Zhang
- Wayen Biotechnologies (Shanghai), Inc., Shanghai, China.,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai, China
| | - Lin Yang
- Department of Clinical Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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11
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Wang B, Guo W, Qiu C, Sun Y, Zhao C, Wu C, Lai X, Feng X. Alveolar macrophage‐derived NRP2 curtails lung injury while boosting host defense in bacterial pneumonia. J Leukoc Biol 2022; 112:499-512. [PMID: 35435271 DOI: 10.1002/jlb.4a1221-770r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/02/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Bing Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital Chinese Academy of Medical Sciences & Peking Union Medical College Tianjin China
| | - Wei Guo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital Chinese Academy of Medical Sciences & Peking Union Medical College Tianjin China
| | - Chen Qiu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital Chinese Academy of Medical Sciences & Peking Union Medical College Tianjin China
| | - Yunyan Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital Chinese Academy of Medical Sciences & Peking Union Medical College Tianjin China
- Department of Hematology, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University Yunnan Cancer Center Kunming China
| | - Chunxiao Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital Chinese Academy of Medical Sciences & Peking Union Medical College Tianjin China
| | - Caihong Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital Chinese Academy of Medical Sciences & Peking Union Medical College Tianjin China
| | - Xun Lai
- Department of Hematology, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University Yunnan Cancer Center Kunming China
| | - Xiaoming Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital Chinese Academy of Medical Sciences & Peking Union Medical College Tianjin China
- Central Laboratory Fujian Medical University Union Hospital Fuzhou China
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12
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Yang J, Do-Umehara HC, Zhang Q, Wang H, Hou C, Dong H, Perez EA, Sala MA, Anekalla KR, Walter JM, Liu S, Wunderink RG, Budinger GRS, Liu J. miR-221-5p-Mediated Downregulation of JNK2 Aggravates Acute Lung Injury. Front Immunol 2021; 12:700933. [PMID: 34899681 PMCID: PMC8656235 DOI: 10.3389/fimmu.2021.700933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/13/2021] [Indexed: 12/24/2022] Open
Abstract
Sepsis and acute lung injury (ALI) are linked to mitochondrial dysfunction; however, the underlying mechanism remains elusive. We previously reported that c-Jun N-terminal protein kinase 2 (JNK2) promotes stress-induced mitophagy by targeting small mitochondrial alternative reading frame (smARF) for ubiquitin-mediated proteasomal degradation, thereby preventing mitochondrial dysfunction and restraining inflammasome activation. Here we report that loss of JNK2 exacerbates lung inflammation and injury during sepsis and ALI in mice. JNK2 is downregulated in mice with endotoxic shock or ALI, concomitantly correlated inversely with disease severity. Small RNA sequencing revealed that miR-221-5p, which contains seed sequence matching to JNK2 mRNA 3’ untranslated region (3’UTR), is upregulated in response to lipopolysaccharide, with dynamically inverse correlation with JNK2 mRNA levels. miR-221-5p targets the 3’UTR of JNK2 mRNA leading to its downregulation. Accordingly, miR-221-5p exacerbates lung inflammation and injury during sepsis in mice by targeting JNK2. Importantly, in patients with pneumonia in medical intensive care unit, JNK2 mRNA levels in alveolar macrophages flow sorted from non-bronchoscopic broncholaveolar lavage (BAL) fluid were inversely correlated strongly and significantly with the percentage of neutrophils, neutrophil and white blood cell counts in BAL fluid. Our data suggest that miR-221-5p targets JNK2 and thereby aggravates lung inflammation and injury during sepsis.
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Affiliation(s)
- Jing Yang
- Department of Surgery, College of Medicine and University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Hanh Chi Do-Umehara
- Department of Surgery, College of Medicine and University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Qiao Zhang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Huashan Wang
- Department of Surgery, College of Medicine and University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Changchun Hou
- Department of Surgery, College of Medicine and University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Huali Dong
- Department of Surgery, College of Medicine and University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Edith A Perez
- Department of Surgery, College of Medicine and University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Marc A Sala
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Kishore R Anekalla
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - James M Walter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China.,State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States.,Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Jing Liu
- Department of Surgery, College of Medicine and University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, United States
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13
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Kitsios GD, Morris A. Seek and Ye Shall Find: COVID-19 and Bacterial Superinfection. Am J Respir Crit Care Med 2021; 204:875-877. [PMID: 34433007 PMCID: PMC8534627 DOI: 10.1164/rccm.202107-1790ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine University of Pittsburgh and University of Pittsburgh Medical Center Pittsburgh, Pennsylvania.,Center for Medicine and the Microbiome.,Acute Lung Injury Center of Excellence University of Pittsburgh Pittsburgh, Pennsylvania
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine University of Pittsburgh and University of Pittsburgh Medical Center Pittsburgh, Pennsylvania.,Center for Medicine and the Microbiome.,Center for Medicine and the Microbiome Acute Lung Injury Center of Excellence.,Department of Immunology University of Pittsburgh Pittsburgh, Pennsylvania
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14
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Pickens CO, Gao CA, Cuttica MJ, Smith SB, Pesce LL, Grant RA, Kang M, Morales-Nebreda L, Bavishi AA, Arnold JM, Pawlowski A, Qi C, Budinger GRS, Singer BD, Wunderink RG. Bacterial Superinfection Pneumonia in Patients Mechanically Ventilated for COVID-19 Pneumonia. Am J Respir Crit Care Med 2021; 204:921-932. [PMID: 34409924 PMCID: PMC8534629 DOI: 10.1164/rccm.202106-1354oc] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Rationale: Current guidelines recommend patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia receive empirical antibiotics for suspected bacterial superinfection on the basis of weak evidence. Rates of ventilator-associated pneumonia (VAP) in clinical trials of patients with SARS-CoV-2 pneumonia are unexpectedly low. Objectives: We conducted an observational single-center study to determine the prevalence and etiology of bacterial superinfection at the time of initial intubation and the incidence and etiology of subsequent bacterial VAP in patients with severe SARS-CoV-2 pneumonia. Methods: Bronchoscopic BAL fluid samples from all patients with SARS-CoV-2 pneumonia requiring mechanical ventilation were analyzed using quantitative cultures and a multiplex PCR panel. Actual antibiotic use was compared with guideline-recommended therapy. Measurements and Main Results: We analyzed 386 BAL samples from 179 patients with SARS-CoV-2 pneumonia requiring mechanical ventilation. Bacterial superinfection within 48 hours of intubation was detected in 21% of patients. Seventy-two patients (44.4%) developed at least one VAP episode (VAP incidence rate = 45.2/1,000 ventilator days); 15 (20.8%) initial VAPs were caused by difficult-to-treat pathogens. The clinical criteria did not distinguish between patients with or without bacterial superinfection. BAL-based management was associated with significantly reduced antibiotic use compared with guideline recommendations. Conclusions: In patients with SARS-CoV-2 pneumonia requiring mechanical ventilation, bacterial superinfection at the time of intubation occurs in <25% of patients. Guideline-based empirical antibiotic management at the time of intubation results in antibiotic overuse. Bacterial VAP developed in 44% of patients and could not be accurately identified in the absence of microbiologic analysis of BAL fluid.
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Affiliation(s)
| | - Catherine A Gao
- Division of Pulmonary and Critical Care, Department of Medicine
| | | | - Sean B Smith
- Division of Pulmonary and Critical Care, Department of Medicine
| | | | - Rogan A Grant
- Division of Pulmonary and Critical Care, Department of Medicine
| | - Mengjia Kang
- Division of Pulmonary and Critical Care, Department of Medicine
| | | | - Avni A Bavishi
- Division of Pulmonary and Critical Care, Department of Medicine
| | - Jason M Arnold
- Division of Pulmonary and Critical Care, Department of Medicine
| | | | - Chao Qi
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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15
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Budinger GS, Misharin AV, Ridge KM, Singer BD, Wunderink RG. Distinctive features of severe SARS-CoV-2 pneumonia. J Clin Invest 2021; 131:149412. [PMID: 34263736 PMCID: PMC8279580 DOI: 10.1172/jci149412] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is among the most important public health crises of our generation. Despite the promise of prevention offered by effective vaccines, patients with severe COVID-19 will continue to populate hospitals and intensive care units for the foreseeable future. The most common clinical presentation of severe COVID-19 is hypoxemia and respiratory failure, typical of the acute respiratory distress syndrome (ARDS). Whether the clinical features and pathobiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia differ from those of pneumonia secondary to other pathogens is unclear. This uncertainty has created variability in the application of historically proven therapies for ARDS to patients with COVID-19. We review the available literature and find many similarities between patients with ARDS from pneumonia attributable to SARS-CoV-2 versus other respiratory pathogens. A notable exception is the long duration of illness among patients with COVID-19, which could result from its unique pathobiology. Available data support the use of care pathways and therapies proven effective for patients with ARDS, while pointing to unique features that might be therapeutically targeted for patients with severe SARS-CoV-2 pneumonia.
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16
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Asymptomatic bacterisputia: Rethinking diagnostic stewardship in pneumonia. Infect Control Hosp Epidemiol 2021; 42:737-739. [PMID: 33934730 DOI: 10.1017/ice.2021.109] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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17
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Jones BE, Jones MM. Pneumonia and Electronic Health Records-A Window Into Disease, A Mirror of Our Behavior, or Just Another Streetlight? Clin Infect Dis 2021; 71:1613-1615. [PMID: 31665250 DOI: 10.1093/cid/ciz1053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 10/21/2019] [Indexed: 12/21/2022] Open
Affiliation(s)
- Barbara Ellen Jones
- Division of Pulmonary and Critical Care Medicine, University of Utah, Salt Lake City, Utah, USA.,IDEAS Center of Innovation, VA Healthcare System, Salt Lake City, Utah, USA
| | - Makoto Murakami Jones
- IDEAS Center of Innovation, VA Healthcare System, Salt Lake City, Utah, USA.,Division of Epidemiology, University of Utah, Salt Lake City, Utah, USA
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18
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Meyer Sauteur PM. Challenges and Progress Toward Determining Pneumonia Etiology. Clin Infect Dis 2021; 71:514-516. [PMID: 31504351 DOI: 10.1093/cid/ciz879] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/02/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Patrick M Meyer Sauteur
- Division of Infectious Diseases and Hospital Epidemiology, University Children's Hospital Zurich, Zurich, Switzerland
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19
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Mraheil MA, Toque HA, La Pietra L, Hamacher J, Phanthok T, Verin A, Gonzales J, Su Y, Fulton D, Eaton DC, Chakraborty T, Lucas R. Dual Role of Hydrogen Peroxide as an Oxidant in Pneumococcal Pneumonia. Antioxid Redox Signal 2021; 34:962-978. [PMID: 32283950 PMCID: PMC8035917 DOI: 10.1089/ars.2019.7964] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Significance:Streptococcus pneumoniae (Spn), a facultative anaerobic Gram-positive human pathogen with increasing rates of penicillin and macrolide resistance, is a major cause of lower respiratory tract infections worldwide. Pneumococci are a primary agent of severe pneumonia in children younger than 5 years and of community-acquired pneumonia in adults. A major defense mechanism toward Spn is the generation of reactive oxygen species, including hydrogen peroxide (H2O2), during the oxidative burst of neutrophils and macrophages. Paradoxically, Spn produces high endogenous levels of H2O2 as a strategy to promote colonization. Recent Advances: Pneumococci, which express neither catalase nor common regulators of peroxide stress resistance, have developed unique mechanisms to protect themselves from H2O2. Spn generates high levels of H2O2 as a strategy to promote colonization. Production of H2O2 moreover constitutes an important virulence phenotype and its cellular activities overlap and complement those of other virulence factors, such as pneumolysin, in modulating host immune responses and promoting organ injury. Critical Issues: This review examines the dual role of H2O2 in pneumococcal pneumonia, from the viewpoint of both the pathogen (defense mechanisms, lytic activity toward competing pathogens, and virulence) and the resulting host-response (inflammasome activation, endoplasmic reticulum stress, and damage to the alveolar-capillary barrier in the lungs). Future Directions: An understanding of the complexity of H2O2-mediated host-pathogen interactions is necessary to develop novel strategies that target these processes to enhance lung function during severe pneumonia.
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Affiliation(s)
- Mobarak Abu Mraheil
- Institute for Medical Microbiology, Justus-Liebig University, Giessen, Germany
| | - Haroldo A Toque
- Vascular Biology Center and Medical College of Georgia at Augusta University, Augusta, Georgia, USA.,Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Luigi La Pietra
- Institute for Medical Microbiology, Justus-Liebig University, Giessen, Germany
| | - Juerg Hamacher
- Internal Medicine and Pneumology, Lindenhofspital, Bern, Switzerland.,Lungen- und Atmungsstiftung Bern, Bern, Switzerland.,Internal Medicine V-Pneumology, Allergology, Respiratory and Environmental Medicine, Faculty of Medicine, Saarland University, Saarbrücken, Germany
| | - Tenzing Phanthok
- Department of Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Alexander Verin
- Vascular Biology Center and Medical College of Georgia at Augusta University, Augusta, Georgia, USA.,Department of Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Joyce Gonzales
- Department of Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Yunchao Su
- Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - David Fulton
- Vascular Biology Center and Medical College of Georgia at Augusta University, Augusta, Georgia, USA.,Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Douglas C Eaton
- Department of Medicine, Emory School of Medicine, Atlanta, Georgia, USA
| | - Trinad Chakraborty
- Institute for Medical Microbiology, Justus-Liebig University, Giessen, Germany
| | - Rudolf Lucas
- Vascular Biology Center and Medical College of Georgia at Augusta University, Augusta, Georgia, USA.,Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA.,Department of Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
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20
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Rhodes NJ, Wunderink RG. Empiric Carbapenems for Nosocomial Pneumonia: Is Hindsight Clearer in 2020? Chest 2021; 159:897-899. [PMID: 33678269 DOI: 10.1016/j.chest.2020.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 12/01/2022] Open
Affiliation(s)
- Nathaniel J Rhodes
- Department of Pharmacy Practice, Chicago College of Pharmacy, and Pharmacometrics Center of Excellence, Midwestern University, Downers Grove, IL; Department of Pharmacy, Northwestern Memorial Hospital, Chicago, IL.
| | - Richard G Wunderink
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
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21
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Akbarpour M, Lecuona E, Chiu SF, Wu Q, Querrey M, Fernandez R, Núñez-Santana FL, Sun H, Ravi S, Kurihara C, Walter JM, Joshi N, Ren Z, Roberts SC, Hauser A, Kreisel D, Li W, Chandel NS, Misharin AV, Mohanakumar T, Budinger GRS, Bharat A. Residual endotoxin induces primary graft dysfunction through ischemia/reperfusion-primed alveolar macrophages. J Clin Invest 2021; 130:4456-4469. [PMID: 32692317 DOI: 10.1172/jci135838] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/13/2020] [Indexed: 12/12/2022] Open
Abstract
Despite the widespread use of antibiotics, bacterial pneumonias in donors strongly predispose to the fatal syndrome of primary graft dysfunction (PGD) following lung transplantation. We report that bacterial endotoxin persists in human donor lungs after pathogen is cleared with antibiotics and is associated with neutrophil infiltration and PGD. In mouse models, depletion of tissue-resident alveolar macrophages (TRAMs) attenuated neutrophil recruitment in response to endotoxin as shown by compartmental staining and intravital imaging. Bone marrow chimeric mice revealed that neutrophils were recruited by TRAM through activation of TLR4 in a MyD88-dependent manner. Intriguingly, low levels of endotoxin, insufficient to cause donor lung injury, promoted TRAM-dependent production of CXCL2, increased neutrophil recruitment, and led to PGD, which was independent of donor NCMs. Reactive oxygen species (ROS) increased in human donor lungs starting from the warm-ischemia phase and were associated with increased transcription and translocation to the plasma membrane of TLR4 in donor TRAMs. Consistently, scavenging ROS or inhibiting their production to prevent TLR4 transcription/translocation or blockade of TLR4 or coreceptor CD14 on donor TRAMs prevented neutrophil recruitment in response to endotoxin and ameliorated PGD. Our studies demonstrate that residual endotoxin after successful treatment of donor bacterial pneumonia promotes PGD through ischemia/reperfusion-primed donor TRAMs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Nikita Joshi
- Division of Pulmonary and Critical Care Medicine, and
| | - Ziyou Ren
- Division of Pulmonary and Critical Care Medicine, and
| | - Scott C Roberts
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Alan Hauser
- Division of Pulmonary and Critical Care Medicine, and.,Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Daniel Kreisel
- Department of Surgery and.,Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri, USA
| | | | | | | | | | | | - Ankit Bharat
- Division of Thoracic Surgery.,Division of Pulmonary and Critical Care Medicine, and
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22
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Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia. Nature 2021; 590:635-641. [PMID: 33429418 PMCID: PMC7987233 DOI: 10.1038/s41586-020-03148-w] [Citation(s) in RCA: 459] [Impact Index Per Article: 153.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/21/2020] [Indexed: 01/29/2023]
Abstract
Some patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop severe pneumonia and acute respiratory distress syndrome1 (ARDS). Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from that in other types of pneumonia2. Here we investigate SARS-CoV-2 pathobiology by characterizing the immune response in the alveoli of patients infected with the virus. We collected bronchoalveolar lavage fluid samples from 88 patients with SARS-CoV-2-induced respiratory failure and 211 patients with known or suspected pneumonia from other pathogens, and analysed them using flow cytometry and bulk transcriptomic profiling. We performed single-cell RNA sequencing on 10 bronchoalveolar lavage fluid samples collected from patients with severe coronavirus disease 2019 (COVID-19) within 48 h of intubation. In the majority of patients with SARS-CoV-2 infection, the alveolar space was persistently enriched in T cells and monocytes. Bulk and single-cell transcriptomic profiling suggested that SARS-CoV-2 infects alveolar macrophages, which in turn respond by producing T cell chemoattractants. These T cells produce interferon-γ to induce inflammatory cytokine release from alveolar macrophages and further promote T cell activation. Collectively, our results suggest that SARS-CoV-2 causes a slowly unfolding, spatially limited alveolitis in which alveolar macrophages containing SARS-CoV-2 and T cells form a positive feedback loop that drives persistent alveolar inflammation.
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23
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Yue Z, Zhang E, Xu C, Khurana S, Batra N, Dang SDH, Cimino JJ, Chen JY. PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies. Nucleic Acids Res 2021; 49:D589-D599. [PMID: 33245774 PMCID: PMC7778959 DOI: 10.1093/nar/gkaa1094] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/23/2020] [Accepted: 10/27/2020] [Indexed: 12/13/2022] Open
Abstract
PAGER-CoV (http://discovery.informatics.uab.edu/PAGER-CoV/) is a new web-based database that can help biomedical researchers interpret coronavirus-related functional genomic study results in the context of curated knowledge of host viral infection, inflammatory response, organ damage, and tissue repair. The new database consists of 11 835 PAGs (Pathways, Annotated gene-lists, or Gene signatures) from 33 public data sources. Through the web user interface, users can search by a query gene or a query term and retrieve significantly matched PAGs with all the curated information. Users can navigate from a PAG of interest to other related PAGs through either shared PAG-to-PAG co-membership relationships or PAG-to-PAG regulatory relationships, totaling 19 996 993. Users can also retrieve enriched PAGs from an input list of COVID-19 functional study result genes, customize the search data sources, and export all results for subsequent offline data analysis. In a case study, we performed a gene set enrichment analysis (GSEA) of a COVID-19 RNA-seq data set from the Gene Expression Omnibus database. Compared with the results using the standard PAGER database, PAGER-CoV allows for more sensitive matching of known immune-related gene signatures. We expect PAGER-CoV to be invaluable for biomedical researchers to find molecular biology mechanisms and tailored therapeutics to treat COVID-19 patients.
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Affiliation(s)
- Zongliang Yue
- Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35223, USA
| | - Eric Zhang
- Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35223, USA
| | - Clark Xu
- University of Wisconsin-Madison School of Medicine and Public Health, Institute of Clinical and Translational Research, Madison, WI 53705-2221, USA
| | - Sunny Khurana
- Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35223, USA
| | - Nishant Batra
- Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35223, USA
| | - Son Do Hai Dang
- Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35223, USA
| | - James J Cimino
- Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35223, USA
| | - Jake Y Chen
- Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35223, USA
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24
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Arabi YM, Mallampalli R, Englert JA, Bosch NA, Walkey AJ, Al-Dorzi HM. Update in Critical Care 2019. Am J Respir Crit Care Med 2020; 201:1050-1057. [PMID: 32176850 DOI: 10.1164/rccm.202002-0285up] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Yaseen M Arabi
- Intensive Care Department, College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Rama Mallampalli
- Division of Pulmonary, Critical Care, and Sleep Medicine, Ohio State Wexner Medical, Center, Columbus, Ohio; and
| | - Joshua A Englert
- Division of Pulmonary, Critical Care, and Sleep Medicine, Ohio State Wexner Medical, Center, Columbus, Ohio; and
| | - Nicholas A Bosch
- Department of Medicine, Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
| | - Allan J Walkey
- Department of Medicine, Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
| | - Hasan M Al-Dorzi
- Intensive Care Department, College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh, Saudi Arabia
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25
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Stoppe C, Wendt S, Mehta NM, Compher C, Preiser JC, Heyland DK, Kristof AS. Biomarkers in critical care nutrition. Crit Care 2020; 24:499. [PMID: 32787899 PMCID: PMC7425162 DOI: 10.1186/s13054-020-03208-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023] Open
Abstract
The goal of nutrition support is to provide the substrates required to match the bioenergetic needs of the patient and promote the net synthesis of macromolecules required for the preservation of lean mass, organ function, and immunity. Contemporary observational studies have exposed the pervasive undernutrition of critically ill patients and its association with adverse clinical outcomes. The intuitive hypothesis is that optimization of nutrition delivery should improve ICU clinical outcomes. It is therefore surprising that multiple large randomized controlled trials have failed to demonstrate the clinical benefit of restoring or maximizing nutrient intake. This may be in part due to the absence of biological markers that identify patients who are most likely to benefit from nutrition interventions and that monitor the effects of nutrition support. Here, we discuss the need for practical risk stratification tools in critical care nutrition, a proposed rationale for targeted biomarker development, and potential approaches that can be adopted for biomarker identification and validation in the field.
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Affiliation(s)
- Christian Stoppe
- 3CARE—Cardiovascular Critical Care & Anesthesia Evaluation and Research, Aachen, Germany
- Department of Anesthesiology, University Hospital RWTH Aachen, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Sebastian Wendt
- 3CARE—Cardiovascular Critical Care & Anesthesia Evaluation and Research, Aachen, Germany
| | - Nilesh M. Mehta
- Department of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Charlene Compher
- Department of Biobehavioral Health Science, University of Pennsylvania and Clinical Nutrition Support Service, Hospital of the University of Pennsylvania, Philadelphia, PA USA
| | - Jean-Charles Preiser
- Erasme University Hospital, Université Libre de Bruxelles, 808 route de Lennik, B-1070 Brussels, Belgium
| | - Daren K. Heyland
- Department of Critical Care Medicine, Queen’s University, Angada 4, Kingston, ON K7L 2V7 Canada
- Clinical Evaluation Research Unit, Kingston General Hospital, Angada 4, Kingston, ON K7L 2V7 Canada
| | - Arnold S. Kristof
- Meakins-Christie Laboratories and Translational Research in Respiratory Diseases Program, Faculty of Medicine, Departments of Medicine and Critical Care, Research Institute of the McGill University Health Centre, 1001 Décarie Blvd., EM3.2219, Montreal, QC H4A 3J1 Canada
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26
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Grant RA, Morales-Nebreda L, Markov NS, Swaminathan S, Guzman ER, Abbott DA, Donnelly HK, Donayre A, Goldberg IA, Klug ZM, Borkowski N, Lu Z, Kihshen H, Politanska Y, Sichizya L, Kang M, Shilatifard A, Qi C, Argento AC, Kruser JM, Malsin ES, Pickens CO, Smith S, Walter JM, Pawlowski AE, Schneider D, Nannapaneni P, Abdala-Valencia H, Bharat A, Gottardi CJ, Budinger GRS, Misharin AV, Singer BD, Wunderink RG. Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.05.238188. [PMID: 34013276 PMCID: PMC8132268 DOI: 10.1101/2020.08.05.238188] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Some patients infected with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) develop severe pneumonia and the acute respiratory distress syndrome (ARDS) [1]. Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from other types of pneumonia [2]. We collected bronchoalveolar lavage fluid samples from 86 patients with SARS-CoV-2-induced respiratory failure and 252 patients with known or suspected pneumonia from other pathogens and subjected them to flow cytometry and bulk transcriptomic profiling. We performed single cell RNA-Seq in 5 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. In the majority of patients with SARS-CoV-2 infection at the onset of mechanical ventilation, the alveolar space is persistently enriched in alveolar macrophages and T cells without neutrophilia. Bulk and single cell transcriptomic profiling suggest SARS-CoV-2 infects alveolar macrophages that respond by recruiting T cells. These T cells release interferon-gamma to induce inflammatory cytokine release from alveolar macrophages and further promote T cell recruitment. Our results suggest SARS-CoV-2 causes a slowly unfolding, spatially-limited alveolitis in which alveolar macrophages harboring SARS-CoV-2 transcripts and T cells form a positive feedback loop that drives progressive alveolar inflammation. This manuscript is accompanied by an online resource: https://www.nupulmonary.org/covid-19/. ONE SENTENCE SUMMARY SARS-CoV-2-infected alveolar macrophages form positive feedback loops with T cells in patients with severe COVID-19.
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27
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Niederman MS, Nair GB, Matt U, Herold S, Pennington K, Crothers K, Cummings M, Schluger NW. Update in Lung Infections and Tuberculosis 2018. Am J Respir Crit Care Med 2020; 200:414-422. [PMID: 31042415 DOI: 10.1164/rccm.201903-0606up] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Michael S Niederman
- 1Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical College, New York Presbyterian/Weill Cornell Medical Center, New York, New York
| | - Girish Balachandran Nair
- 2Division of Pulmonary and Critical Care Medicine, Beaumont Health, William Beaumont School of Medicine, Oakland University, Royal Oak, Michigan
| | - Ulrich Matt
- 3Department of Internal Medicine II, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research, Justus Liebig University, Giessen, Germany
| | - Susanne Herold
- 3Department of Internal Medicine II, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research, Justus Liebig University, Giessen, Germany
| | - Kelly Pennington
- 4Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Kristina Crothers
- 5Pulmonary, Critical Care and Sleep Medicine, VA Puget Sound Health Care System, Seattle, Washington.,6University of Washington, Seattle, Washington; and
| | | | - Neil W Schluger
- 7Columbia University Irving Medical Center, New York, New York
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28
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Torres A, Barberán J, Ceccato A, Martin-Loeches I, Ferrer M, Menéndez R, Rigau D. Neumonía intrahospitalaria. Normativa de la Sociedad Española de Neumología y Cirugía Torácica (SEPAR). Actualización 2020. Arch Bronconeumol 2020. [DOI: 10.1016/j.arbres.2020.01.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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29
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Baschal EE, Larson ED, Bootpetch Roberts TC, Pathak S, Frank G, Handley E, Dinwiddie J, Moloney M, Yoon PJ, Gubbels SP, Scholes MA, Cass SP, Jenkins HA, Frank DN, Yang IV, Schwartz DA, Ramakrishnan VR, Santos-Cortez RLP. Identification of Novel Genes and Biological Pathways That Overlap in Infectious and Nonallergic Diseases of the Upper and Lower Airways Using Network Analyses. Front Genet 2020; 10:1352. [PMID: 32010199 PMCID: PMC6979043 DOI: 10.3389/fgene.2019.01352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022] Open
Abstract
Previous genetic studies on susceptibility to otitis media and airway infections have focused on immune pathways acting within the local mucosal epithelium, and outside of allergic rhinitis and asthma, limited studies exist on the overlaps at the gene, pathway or network level between the upper and lower airways. In this report, we compared [1] pathways identified from network analysis using genes derived from published genome-wide family-based and association studies for otitis media, sinusitis, and lung phenotypes, to [2] pathways identified using differentially expressed genes from RNA-sequence data from lower airway, sinus, and middle ear tissues, in particular cholesteatoma tissue compared to middle ear mucosa. For otitis media, a large number of genes (n = 1,806) were identified as differentially expressed between cholesteatoma and middle ear mucosa, which in turn led to the identification of 68 pathways that are enriched in cholesteatoma. Two differentially expressed genes CR1 and SAA1 overlap in middle ear, sinus, and lower airway samples and are potentially novel genes for otitis media susceptibility. In addition, 56 genes were differentially expressed in both tissues from the middle ear and either sinus or lower airways. Pathways that are common in upper and lower airway diseases, whether from published DNA studies or from our RNA-sequencing analyses, include chromatin organization/remodeling, endocytosis, immune system process, protein folding, and viral process. Taken together, our findings from genetic susceptibility and differential tissue expression studies support the hypothesis that the unified airway theory wherein the upper and lower respiratory tracts act as an integrated unit also applies to infectious and nonallergic airway epithelial disease. Our results may be used as reference for identification of genes or pathways that are relevant to upper and lower airways, whether common across sites, or unique to each disease.
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Affiliation(s)
- Erin E Baschal
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Eric D Larson
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Tori C Bootpetch Roberts
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Shivani Pathak
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Gretchen Frank
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Elyse Handley
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Jordyn Dinwiddie
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Molly Moloney
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Patricia J Yoon
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Samuel P Gubbels
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Melissa A Scholes
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Stephen P Cass
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Herman A Jenkins
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Daniel N Frank
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ivana V Yang
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - David A Schwartz
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Vijay R Ramakrishnan
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Regie Lyn P Santos-Cortez
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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30
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Yang L, Haidar G, Zia H, Nettles R, Qin S, Wang X, Shah F, Rapport SF, Charalampous T, Methé B, Fitch A, Morris A, McVerry BJ, O'Grady J, Kitsios GD. Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study. Respir Res 2019; 20:265. [PMID: 31775777 PMCID: PMC6882222 DOI: 10.1186/s12931-019-1218-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/15/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Metagenomic sequencing of respiratory microbial communities for pathogen identification in pneumonia may help overcome the limitations of culture-based methods. We examined the feasibility and clinical validity of rapid-turnaround metagenomics with Nanopore™ sequencing of clinical respiratory specimens. METHODS We conducted a case-control study of mechanically-ventilated patients with pneumonia (nine culture-positive and five culture-negative) and without pneumonia (eight controls). We collected endotracheal aspirates and applied a microbial DNA enrichment method prior to metagenomic sequencing with the Oxford Nanopore MinION device. For reference, we compared Nanopore results against clinical microbiologic cultures and bacterial 16S rRNA gene sequencing. RESULTS Human DNA depletion enabled in depth sequencing of microbial communities. In culture-positive cases, Nanopore revealed communities with high abundance of the bacterial or fungal species isolated by cultures. In four cases with resistant clinical isolates, Nanopore detected antibiotic resistance genes corresponding to the phenotypic resistance in antibiograms. In culture-negative pneumonia, Nanopore revealed probable bacterial pathogens in 1/5 cases and Candida colonization in 3/5 cases. In controls, Nanopore showed high abundance of oral bacteria in 5/8 subjects, and identified colonizing respiratory pathogens in other subjects. Nanopore and 16S sequencing showed excellent concordance for the most abundant bacterial taxa. CONCLUSIONS We demonstrated technical feasibility and proof-of-concept clinical validity of Nanopore metagenomics for severe pneumonia diagnosis, with striking concordance with positive microbiologic cultures, and clinically actionable information obtained from sequencing in culture-negative samples. Prospective studies with real-time metagenomics are warranted to examine the impact on antimicrobial decision-making and clinical outcomes.
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Affiliation(s)
- Libing Yang
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, UPMC Montefiore Hospital, NW628, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Ghady Haidar
- Division of Infectious Diseases, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Haris Zia
- Internal Medicine Residency Program, University of Pittsburgh Medical Center McKeesport, McKeesport, PA, USA
| | - Rachel Nettles
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shulin Qin
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, UPMC Montefiore Hospital, NW628, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Xiaohong Wang
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, UPMC Montefiore Hospital, NW628, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, UPMC Montefiore Hospital, NW628, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - Sarah F Rapport
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, UPMC Montefiore Hospital, NW628, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Themoula Charalampous
- Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Barbara Methé
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, UPMC Montefiore Hospital, NW628, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Adam Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alison Morris
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, UPMC Montefiore Hospital, NW628, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Bryan J McVerry
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, UPMC Montefiore Hospital, NW628, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Justin O'Grady
- Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Norwich, UK
- Quadram Institute Bioscience and University of East Anglia, Norwich, UK
| | - Georgios D Kitsios
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA.
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, UPMC Montefiore Hospital, NW628, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA.
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31
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Gautam S, Sharma L, Dela Cruz CS. Teaching an Old Intensivist Neutrophil Tricks: Using Alveolar Neutrophilia to Diagnose Ventilator-associated Pneumonia. Am J Respir Crit Care Med 2019; 199:1178-1181. [PMID: 30543457 PMCID: PMC6519853 DOI: 10.1164/rccm.201811-2163ed] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Samir Gautam
- 1 Section of Pulmonary, Critical Care, and Sleep Medicine Yale University School of Medicine New Haven, Connecticut
| | - Lokesh Sharma
- 1 Section of Pulmonary, Critical Care, and Sleep Medicine Yale University School of Medicine New Haven, Connecticut
| | - Charles S Dela Cruz
- 1 Section of Pulmonary, Critical Care, and Sleep Medicine Yale University School of Medicine New Haven, Connecticut
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